The boot manager was probably LILO, which is what Mandrake uses by default... or did with 8.0 at least. There are about 3 different ways to install LILO, the last of which I use constantly is probably what you are referring to... installing on the MBR.
Time out for acronyms:
LILO: LInux LOader
MBR: Master Boot Record, the first few sectors of the FIRST hard drive that BIOS will hand off to if its in BIOS's boot order.
That's why LILO wask on disk 1 when Linux was on disk 2. An MBR installation of LILO will put it on the very front of the first hard drive because that's all that BIOS is smart enough to hand the job off to.
I don't know why you had a problem scraping LILO off before... Typically if you install say... I dunno, Windows for instance, it will over-write the MBR in a heartbeat, format the whole thing... basically take over that disk's world if you want to let it. It shouldn't be a problem. If there is a problem, it might be a problem of boot order. For instance, if you have the order:
Then if you pop in a CD, then it'll never get a chance to spin on boot because LILO on the Hard drive will get a chance to interrupt it. You might want to poke 'round your BIOS a bit.
Hope that clears some things up,